There currently no support to change the location of the configuraiton folder, the agent expects it to be in a conf folder relative to the root of the agent files. Updated the RPM using the same symlink solution applied for logs folder. The configuration will be effectively stored in /etc, as per RHEL guidelines.
A /etc/jboss-on/agent folder is created during RPM installation to store
configuration files. A symlink /usr/share/jboss-on-${version}.GA/agent/conf pointing to /etc/jboss-on/agent is also created during installation.